Disease resistance is an important trait in agriculture, particularly for the production of food crops. Although disease resistance alleles have been identified in uncultivated tomato lines, efforts to introduce these alleles into cultivated lines are hindered by the introduction of deleterious traits together with the resistance alleles. The use of marker-assisted selection (MAS) in plant breeding methods has made it possible to select plants based on genetic markers linked to traits of interest. However, accurate markers for identifying or tracking desirable traits in plants are frequently unavailable even if a gene associated with the trait has been characterized. These difficulties are further complicated by factors such as polygenic or quantitative inheritance, and an often incomplete understanding of the genetic background underlying expression of a desired phenotype. Therefore, in the absence of accurate and validated markers for use in MAS, it may not be feasible to produce new plant lines exhibiting certain disease-resistant phenotypes.